Hi Gershon,
I know that @emdupre is working on integrating multi-echo denoising (in addition to optimal combination) with tedana into fMRIPrep, but that’s a little ways out.
I agree that, in the mean time, it makes sense to use fMRIPrep and tedana separately, but within the same overall pipeline. However, I’m not sure about the details of your approach. Specifically, I don’t think you can break fMRIPrep into separate parts like that.
The approach we’re planning to take in a tedana analysis is to run fMRIPrep and then to grab native-space partially preprocessed data (i.e., post STC and HMC) from the fMRIPrep working directory. We’ll then feed those data through tedana and finally apply fMRIPrep’s calculated transforms for coregistration and normalization. We haven’t completed the code to do this yet, but I believe that it’s all doable. The overall pipeline is the same as yours, but doesn’t require stopping and restarting fMRIPrep.
Best,
Taylor